Starting phenix.real_space_refine on Fri Jul 3 09:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dyr_30923/07_2026/7dyr_30923.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8667 2.51 5 N 2229 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "Z" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1814 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "F" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain: "G" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 502 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13326 At special positions: 0 Unit cell: (120.954, 128.381, 85.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2349 8.00 N 2229 7.00 C 8667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 583.7 milliseconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 3 sheets defined 77.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR Y 37 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY Y 49 " --> pdb=" O ASP Y 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 117 Processing helix chain 'Y' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP Y 129 " --> pdb=" O ASP Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 143 Processing helix chain 'Y' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL Y 151 " --> pdb=" O GLN Y 147 " (cutoff:3.500A) Proline residue: Y 154 - end of helix removed outlier: 3.808A pdb=" N ALA Y 159 " --> pdb=" O ALA Y 155 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 171 removed outlier: 3.727A pdb=" N ASN Y 169 " --> pdb=" O SER Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN Y 183 " --> pdb=" O THR Y 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET Y 188 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL Y 190 " --> pdb=" O GLY Y 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL Y 191 " --> pdb=" O GLY Y 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR Y 194 " --> pdb=" O VAL Y 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR Y 211 " --> pdb=" O MET Y 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Y 220 " --> pdb=" O THR Y 216 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 Processing helix chain 'Z' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG Z 22 " --> pdb=" O GLN Z 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Z 24 " --> pdb=" O ASP Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 99 Processing helix chain 'Z' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.512A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER Z 144 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Z 145 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP Z 178 " --> pdb=" O SER Z 174 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 183 No H-bonds generated for 'chain 'Z' and resid 181 through 183' Processing helix chain 'Z' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS Z 190 " --> pdb=" O GLY Z 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN Z 208 " --> pdb=" O GLY Z 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR Z 211 " --> pdb=" O VAL Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 234 through 242 Processing helix chain 'Z' and resid 244 through 260 Processing helix chain 'Z' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE Z 267 " --> pdb=" O ASN Z 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 24 Processing helix chain 'A' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.868A pdb=" N GLY B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.543A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.808A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 192 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.595A pdb=" N HIS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 99 Processing helix chain 'C' and resid 106 through 127 removed outlier: 3.715A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.512A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 244 through 260 Processing helix chain 'C' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.634A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 4.334A pdb=" N THR E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.869A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 4.183A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.542A pdb=" N LEU E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.662A pdb=" N ASP E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.229A pdb=" N GLN E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.808A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.726A pdb=" N ASN E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 202 removed outlier: 4.323A pdb=" N ASN E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 188 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 191 " --> pdb=" O GLY E 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL E 192 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 220 removed outlier: 3.635A pdb=" N TYR E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 220 " --> pdb=" O THR E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.549A pdb=" N ARG F 22 " --> pdb=" O GLN F 18 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 41 through 49 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.784A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.594A pdb=" N HIS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 99 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.716A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.512A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 129 through 145 removed outlier: 4.375A pdb=" N SER F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 180 removed outlier: 3.520A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 186 through 211 removed outlier: 3.777A pdb=" N LYS F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR F 211 " --> pdb=" O VAL F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 244 through 260 Processing helix chain 'F' and resid 263 through 281 removed outlier: 3.632A pdb=" N ILE F 267 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 28 through 52 removed outlier: 3.680A pdb=" N ALA G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR Z 232 " --> pdb=" O VAL Z 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR C 232 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 218 through 221 removed outlier: 7.009A pdb=" N THR F 232 " --> pdb=" O VAL F 219 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4269 1.34 - 1.46: 2665 1.46 - 1.58: 6509 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 13590 Sorted by residual: bond pdb=" N GLN F 41 " pdb=" CA GLN F 41 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.59e+00 bond pdb=" N GLN C 41 " pdb=" CA GLN C 41 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" CB PRO Z 132 " pdb=" CG PRO Z 132 " ideal model delta sigma weight residual 1.492 1.406 0.086 5.00e-02 4.00e+02 2.93e+00 bond pdb=" CB PRO C 132 " pdb=" CG PRO C 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.92e+00 bond pdb=" CB PRO F 132 " pdb=" CG PRO F 132 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.91e+00 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17977 1.97 - 3.94: 413 3.94 - 5.91: 83 5.91 - 7.89: 16 7.89 - 9.86: 9 Bond angle restraints: 18498 Sorted by residual: angle pdb=" N VAL E 156 " pdb=" CA VAL E 156 " pdb=" C VAL E 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL Y 156 " pdb=" CA VAL Y 156 " pdb=" C VAL Y 156 " ideal model delta sigma weight residual 111.81 108.08 3.73 8.60e-01 1.35e+00 1.88e+01 angle pdb=" N VAL B 156 " pdb=" CA VAL B 156 " pdb=" C VAL B 156 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" C GLN Z 41 " pdb=" CA GLN Z 41 " pdb=" CB GLN Z 41 " ideal model delta sigma weight residual 111.48 105.78 5.70 1.59e+00 3.96e-01 1.29e+01 angle pdb=" CA TYR A 73 " pdb=" CB TYR A 73 " pdb=" CG TYR A 73 " ideal model delta sigma weight residual 113.90 107.46 6.44 1.80e+00 3.09e-01 1.28e+01 ... (remaining 18493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7016 17.78 - 35.56: 644 35.56 - 53.34: 194 53.34 - 71.12: 29 71.12 - 88.90: 4 Dihedral angle restraints: 7887 sinusoidal: 2913 harmonic: 4974 Sorted by residual: dihedral pdb=" CA ILE B 174 " pdb=" C ILE B 174 " pdb=" N PRO B 175 " pdb=" CA PRO B 175 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ILE E 174 " pdb=" C ILE E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE Y 174 " pdb=" C ILE Y 174 " pdb=" N PRO Y 175 " pdb=" CA PRO Y 175 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1715 0.052 - 0.104: 424 0.104 - 0.157: 78 0.157 - 0.209: 8 0.209 - 0.261: 1 Chirality restraints: 2226 Sorted by residual: chirality pdb=" CA ASP Z 103 " pdb=" N ASP Z 103 " pdb=" C ASP Z 103 " pdb=" CB ASP Z 103 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO B 72 " pdb=" N PRO B 72 " pdb=" C PRO B 72 " pdb=" CB PRO B 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2223 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO Y 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 71 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 72 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 71 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO E 72 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.050 5.00e-02 4.00e+02 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2180 2.74 - 3.28: 13533 3.28 - 3.82: 22248 3.82 - 4.36: 26647 4.36 - 4.90: 46236 Nonbonded interactions: 110844 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 125 " pdb=" NH2 ARG Z 39 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP E 125 " pdb=" NH2 ARG F 39 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP B 125 " pdb=" NH2 ARG C 39 " model vdw 2.206 3.120 nonbonded pdb=" N ASN G 67 " pdb=" OD1 ASN G 67 " model vdw 2.275 3.120 nonbonded pdb=" N ASN D 67 " pdb=" OD1 ASN D 67 " model vdw 2.275 3.120 ... (remaining 110839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'Y' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'Z' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 13590 Z= 0.325 Angle : 0.779 9.857 18498 Z= 0.420 Chirality : 0.047 0.261 2226 Planarity : 0.006 0.091 2328 Dihedral : 15.446 88.905 4731 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer: Outliers : 3.56 % Allowed : 20.33 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1773 helix: 0.95 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -2.35 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 54 TYR 0.027 0.003 TYR A 73 PHE 0.011 0.001 PHE C 47 TRP 0.011 0.001 TRP E 138 HIS 0.004 0.001 HIS Y 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.32 (13590) covalent geometry : angle 0.77939 / 0.42 (18498) hydrogen bonds : bond 0.14245 / 9.73 ( 888) hydrogen bonds : angle 5.94953 / 4.25 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.473 Fit side-chains REVERT: Y 26 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7372 (mm-30) REVERT: Y 64 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: Y 125 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: Y 176 GLU cc_start: 0.7067 (tp30) cc_final: 0.6789 (tm-30) REVERT: Z 17 THR cc_start: 0.7504 (m) cc_final: 0.7291 (p) REVERT: Z 38 GLU cc_start: 0.8653 (tt0) cc_final: 0.7953 (tt0) REVERT: Z 60 ASN cc_start: 0.6699 (m-40) cc_final: 0.6131 (t0) REVERT: Z 73 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6989 (mt-10) REVERT: Z 94 GLU cc_start: 0.7693 (tt0) cc_final: 0.7217 (tt0) REVERT: Z 175 LYS cc_start: 0.7153 (tptm) cc_final: 0.6931 (tptp) REVERT: Z 223 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7239 (m) REVERT: Z 230 HIS cc_start: 0.7483 (m90) cc_final: 0.7028 (m90) REVERT: A 50 ASP cc_start: 0.6889 (m-30) cc_final: 0.6620 (m-30) REVERT: A 55 ASN cc_start: 0.8150 (p0) cc_final: 0.7944 (p0) REVERT: B 26 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 64 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: B 125 ASP cc_start: 0.7305 (m-30) cc_final: 0.6880 (m-30) REVERT: B 201 MET cc_start: 0.8138 (mtm) cc_final: 0.7772 (mtp) REVERT: C 15 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7833 (ptpp) REVERT: C 17 THR cc_start: 0.7845 (m) cc_final: 0.7635 (p) REVERT: C 20 ASP cc_start: 0.7632 (m-30) cc_final: 0.7260 (m-30) REVERT: C 22 ARG cc_start: 0.6328 (mtp180) cc_final: 0.6116 (mtm110) REVERT: C 38 GLU cc_start: 0.8625 (tt0) cc_final: 0.8073 (tt0) REVERT: C 60 ASN cc_start: 0.6867 (m-40) cc_final: 0.6507 (t0) REVERT: C 73 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7205 (mt-10) REVERT: D 50 ASP cc_start: 0.7159 (m-30) cc_final: 0.6647 (m-30) REVERT: D 55 ASN cc_start: 0.8316 (p0) cc_final: 0.7979 (p0) REVERT: E 3 ILE cc_start: 0.7863 (mt) cc_final: 0.7514 (mm) REVERT: E 4 THR cc_start: 0.7488 (p) cc_final: 0.7264 (t) REVERT: E 130 ASN cc_start: 0.8118 (m110) cc_final: 0.7796 (m-40) REVERT: E 142 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 176 GLU cc_start: 0.7063 (tp30) cc_final: 0.6785 (tm-30) REVERT: E 180 ASN cc_start: 0.7838 (m-40) cc_final: 0.7495 (m-40) REVERT: E 244 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7980 (ttpp) REVERT: F 17 THR cc_start: 0.7743 (m) cc_final: 0.7460 (p) REVERT: F 38 GLU cc_start: 0.8654 (tt0) cc_final: 0.8036 (tt0) REVERT: F 60 ASN cc_start: 0.6881 (m-40) cc_final: 0.6221 (t0) REVERT: F 73 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7015 (mt-10) REVERT: F 95 GLN cc_start: 0.7180 (mp10) cc_final: 0.6768 (mp-120) REVERT: F 102 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6931 (mm) REVERT: F 108 ASN cc_start: 0.7986 (m-40) cc_final: 0.7752 (m-40) REVERT: F 189 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: F 193 GLU cc_start: 0.7609 (tt0) cc_final: 0.7397 (tt0) REVERT: F 259 ARG cc_start: 0.6852 (tpp80) cc_final: 0.6457 (ttp80) REVERT: F 281 CYS cc_start: 0.7790 (m) cc_final: 0.7579 (m) REVERT: G 19 TRP cc_start: 0.6334 (t60) cc_final: 0.6107 (t60) outliers start: 49 outliers final: 13 residues processed: 317 average time/residue: 0.5126 time to fit residues: 178.0345 Evaluate side-chains 241 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 64 MET Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 29 ASN A 15 ASN A 42 GLN C 108 ASN C 158 ASN D 15 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.076029 restraints weight = 17971.499| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.68 r_work: 0.2874 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13590 Z= 0.168 Angle : 0.628 6.549 18498 Z= 0.332 Chirality : 0.043 0.175 2226 Planarity : 0.006 0.089 2328 Dihedral : 5.983 56.154 1904 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.49 % Favored : 93.34 % Rotamer: Outliers : 3.63 % Allowed : 17.36 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.21), residues: 1773 helix: 1.28 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Z 131 TYR 0.026 0.002 TYR A 73 PHE 0.014 0.001 PHE C 157 TRP 0.010 0.001 TRP C 127 HIS 0.003 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13590) covalent geometry : angle 0.62795 / 0.33 (18498) hydrogen bonds : bond 0.05324 / 3.63 ( 888) hydrogen bonds : angle 4.27994 / 3.07 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: Z 60 ASN cc_start: 0.7193 (m-40) cc_final: 0.6817 (t0) REVERT: Z 94 GLU cc_start: 0.8840 (tt0) cc_final: 0.8452 (tt0) REVERT: Z 223 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7476 (m) REVERT: Z 230 HIS cc_start: 0.8006 (m90) cc_final: 0.7731 (m90) REVERT: Z 259 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7990 (ttp80) REVERT: B 26 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8286 (mm-30) REVERT: C 17 THR cc_start: 0.8722 (m) cc_final: 0.8485 (p) REVERT: C 20 ASP cc_start: 0.8748 (m-30) cc_final: 0.8510 (m-30) REVERT: C 38 GLU cc_start: 0.9030 (tt0) cc_final: 0.8769 (tt0) REVERT: C 60 ASN cc_start: 0.7219 (m-40) cc_final: 0.7002 (t0) REVERT: D 16 ASN cc_start: 0.8276 (m-40) cc_final: 0.8048 (m-40) REVERT: E 176 GLU cc_start: 0.7378 (tp30) cc_final: 0.7008 (tm-30) REVERT: F 38 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8830 (tt0) REVERT: F 95 GLN cc_start: 0.8410 (mp10) cc_final: 0.8065 (mp-120) REVERT: F 183 MET cc_start: 0.6545 (mmm) cc_final: 0.6293 (mmm) REVERT: F 189 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: G 19 TRP cc_start: 0.6738 (t60) cc_final: 0.6423 (t60) outliers start: 50 outliers final: 17 residues processed: 269 average time/residue: 0.5603 time to fit residues: 164.7945 Evaluate side-chains 237 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 15 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 29 ASN F 108 ASN F 158 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.075254 restraints weight = 18070.285| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.69 r_work: 0.2860 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13590 Z= 0.165 Angle : 0.607 6.852 18498 Z= 0.322 Chirality : 0.043 0.176 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.516 59.283 1888 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer: Outliers : 3.34 % Allowed : 17.50 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1773 helix: 1.41 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.46 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.027 0.002 TYR A 73 PHE 0.012 0.001 PHE F 47 TRP 0.010 0.001 TRP Z 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (13590) covalent geometry : angle 0.60703 / 0.32 (18498) hydrogen bonds : bond 0.05191 / 3.53 ( 888) hydrogen bonds : angle 4.11010 / 2.95 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: Y 176 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: Z 94 GLU cc_start: 0.8842 (tt0) cc_final: 0.8485 (tt0) REVERT: Z 223 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7453 (m) REVERT: Z 230 HIS cc_start: 0.7990 (m90) cc_final: 0.7717 (m90) REVERT: B 26 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8259 (mm-30) REVERT: C 38 GLU cc_start: 0.9022 (tt0) cc_final: 0.8778 (tt0) REVERT: D 16 ASN cc_start: 0.8242 (m-40) cc_final: 0.8019 (m-40) REVERT: D 29 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5948 (tm) REVERT: E 64 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8732 (mtp) REVERT: E 176 GLU cc_start: 0.7324 (tp30) cc_final: 0.6992 (tm-30) REVERT: F 38 GLU cc_start: 0.9136 (tt0) cc_final: 0.8877 (tt0) REVERT: F 95 GLN cc_start: 0.8423 (mp10) cc_final: 0.8073 (mp-120) REVERT: F 183 MET cc_start: 0.6692 (mmm) cc_final: 0.6410 (mmm) REVERT: F 189 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: G 19 TRP cc_start: 0.6720 (t60) cc_final: 0.6410 (t60) outliers start: 46 outliers final: 23 residues processed: 271 average time/residue: 0.5898 time to fit residues: 174.8227 Evaluate side-chains 255 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 4 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 176 GLU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 163 optimal weight: 0.2980 chunk 46 optimal weight: 0.0970 chunk 153 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 60 ASN A 15 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 108 ASN F 189 GLN G 11 ASN G 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.075837 restraints weight = 18051.028| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.69 r_work: 0.2869 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13590 Z= 0.156 Angle : 0.589 7.812 18498 Z= 0.313 Chirality : 0.042 0.170 2226 Planarity : 0.006 0.087 2328 Dihedral : 5.545 58.729 1888 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.09 % Favored : 93.74 % Rotamer: Outliers : 2.90 % Allowed : 18.37 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.21), residues: 1773 helix: 1.56 (0.15), residues: 1314 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 64 TYR 0.025 0.002 TYR A 73 PHE 0.012 0.001 PHE F 47 TRP 0.009 0.001 TRP Z 127 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13590) covalent geometry : angle 0.58950 / 0.31 (18498) hydrogen bonds : bond 0.04893 / 3.32 ( 888) hydrogen bonds : angle 4.00605 / 2.88 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: Y 125 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: Z 60 ASN cc_start: 0.6945 (m-40) cc_final: 0.6489 (t0) REVERT: Z 223 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7406 (m) REVERT: Z 230 HIS cc_start: 0.7973 (m90) cc_final: 0.7676 (m90) REVERT: B 26 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8250 (mm-30) REVERT: B 166 GLU cc_start: 0.6645 (pm20) cc_final: 0.6359 (pm20) REVERT: B 170 MET cc_start: 0.6991 (ttm) cc_final: 0.6787 (mtm) REVERT: C 38 GLU cc_start: 0.9023 (tt0) cc_final: 0.8812 (tt0) REVERT: D 16 ASN cc_start: 0.8171 (m-40) cc_final: 0.7946 (m-40) REVERT: D 29 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6227 (tm) REVERT: E 176 GLU cc_start: 0.7204 (tp30) cc_final: 0.6842 (tm-30) REVERT: F 38 GLU cc_start: 0.9111 (tt0) cc_final: 0.8875 (tt0) REVERT: F 95 GLN cc_start: 0.8421 (mp10) cc_final: 0.8042 (mp-120) REVERT: F 183 MET cc_start: 0.6696 (mmm) cc_final: 0.6409 (mmm) REVERT: F 189 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: G 19 TRP cc_start: 0.6794 (t60) cc_final: 0.6426 (t60) outliers start: 40 outliers final: 19 residues processed: 265 average time/residue: 0.5733 time to fit residues: 166.3403 Evaluate side-chains 246 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 1.9990 chunk 164 optimal weight: 0.0670 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.099589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.074434 restraints weight = 18070.550| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.70 r_work: 0.2842 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13590 Z= 0.179 Angle : 0.619 9.693 18498 Z= 0.329 Chirality : 0.043 0.187 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.590 58.463 1888 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 3.27 % Allowed : 17.79 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1773 helix: 1.66 (0.15), residues: 1311 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Z 64 TYR 0.028 0.002 TYR A 73 PHE 0.014 0.001 PHE F 47 TRP 0.011 0.001 TRP F 127 HIS 0.004 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13590) covalent geometry : angle 0.61895 / 0.33 (18498) hydrogen bonds : bond 0.05287 / 3.59 ( 888) hydrogen bonds : angle 4.03412 / 2.91 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8248 (mtmt) REVERT: Y 58 MET cc_start: 0.9100 (mmm) cc_final: 0.8543 (mmp) REVERT: Y 125 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: Z 187 PHE cc_start: 0.8163 (t80) cc_final: 0.7944 (t80) REVERT: Z 223 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7409 (m) REVERT: Z 230 HIS cc_start: 0.7997 (m90) cc_final: 0.7673 (m90) REVERT: A 29 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6290 (tm) REVERT: B 26 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8200 (mm-30) REVERT: C 38 GLU cc_start: 0.9048 (tt0) cc_final: 0.8830 (tt0) REVERT: D 16 ASN cc_start: 0.8131 (m-40) cc_final: 0.7836 (m-40) REVERT: D 29 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6135 (tm) REVERT: E 64 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8577 (mtt) REVERT: F 38 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: F 95 GLN cc_start: 0.8402 (mp10) cc_final: 0.8127 (mp-120) REVERT: F 183 MET cc_start: 0.6693 (mmm) cc_final: 0.6406 (mmm) REVERT: F 189 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: G 19 TRP cc_start: 0.6865 (t60) cc_final: 0.6476 (t60) outliers start: 45 outliers final: 23 residues processed: 259 average time/residue: 0.5686 time to fit residues: 161.2177 Evaluate side-chains 252 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 174 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 160 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 138 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 60 ASN A 15 ASN B 180 ASN C 98 ASN C 108 ASN D 11 ASN D 15 ASN E 121 GLN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.076658 restraints weight = 17963.952| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.67 r_work: 0.2882 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13590 Z= 0.145 Angle : 0.580 10.736 18498 Z= 0.307 Chirality : 0.042 0.164 2226 Planarity : 0.006 0.087 2328 Dihedral : 5.490 56.759 1888 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 3.05 % Allowed : 18.30 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.21), residues: 1773 helix: 1.80 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -2.41 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.023 0.002 TYR A 73 PHE 0.013 0.001 PHE F 47 TRP 0.009 0.001 TRP F 127 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13590) covalent geometry : angle 0.58044 / 0.31 (18498) hydrogen bonds : bond 0.04664 / 3.16 ( 888) hydrogen bonds : angle 3.93180 / 2.83 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8297 (mtmt) REVERT: Y 125 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: Y 244 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8332 (ttpp) REVERT: Z 187 PHE cc_start: 0.8137 (t80) cc_final: 0.7870 (t80) REVERT: Z 223 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7353 (m) REVERT: Z 230 HIS cc_start: 0.7993 (m90) cc_final: 0.7670 (m90) REVERT: A 29 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6250 (tm) REVERT: B 26 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8196 (mm-30) REVERT: B 47 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8327 (tttp) REVERT: D 16 ASN cc_start: 0.8150 (m-40) cc_final: 0.7898 (m-40) REVERT: D 29 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6090 (tm) REVERT: E 47 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8492 (tttt) REVERT: F 95 GLN cc_start: 0.8406 (mp10) cc_final: 0.8046 (mp-120) REVERT: F 183 MET cc_start: 0.6669 (mmm) cc_final: 0.6379 (mmm) REVERT: F 189 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: G 19 TRP cc_start: 0.6889 (t60) cc_final: 0.6490 (t60) outliers start: 42 outliers final: 24 residues processed: 265 average time/residue: 0.5667 time to fit residues: 164.6103 Evaluate side-chains 254 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 125 ASP Chi-restraints excluded: chain Y residue 174 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 60 ASN A 15 ASN B 130 ASN C 98 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.074615 restraints weight = 18021.530| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.68 r_work: 0.2843 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13590 Z= 0.178 Angle : 0.615 9.009 18498 Z= 0.327 Chirality : 0.043 0.182 2226 Planarity : 0.006 0.087 2328 Dihedral : 5.541 55.726 1888 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 3.27 % Allowed : 18.30 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1773 helix: 1.74 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.34 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 39 TYR 0.027 0.002 TYR D 73 PHE 0.015 0.001 PHE F 47 TRP 0.012 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (13590) covalent geometry : angle 0.61459 / 0.33 (18498) hydrogen bonds : bond 0.05180 / 3.52 ( 888) hydrogen bonds : angle 3.98818 / 2.87 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8339 (mtmt) REVERT: Y 58 MET cc_start: 0.9053 (mmm) cc_final: 0.8562 (mmp) REVERT: Y 125 ASP cc_start: 0.8432 (m-30) cc_final: 0.8208 (m-30) REVERT: Y 244 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: Z 60 ASN cc_start: 0.7110 (m-40) cc_final: 0.6588 (t0) REVERT: Z 61 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7233 (p0) REVERT: Z 187 PHE cc_start: 0.8154 (t80) cc_final: 0.7897 (t80) REVERT: Z 223 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7338 (m) REVERT: Z 230 HIS cc_start: 0.7998 (m90) cc_final: 0.7734 (m-70) REVERT: A 29 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6355 (tm) REVERT: B 26 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 47 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8314 (tttp) REVERT: B 172 ASN cc_start: 0.6327 (m-40) cc_final: 0.6115 (m-40) REVERT: D 16 ASN cc_start: 0.8107 (m-40) cc_final: 0.7832 (m-40) REVERT: D 29 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6109 (tm) REVERT: F 95 GLN cc_start: 0.8394 (mp10) cc_final: 0.8039 (mp-120) REVERT: F 183 MET cc_start: 0.6722 (mmm) cc_final: 0.6408 (mmm) REVERT: F 189 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: G 19 TRP cc_start: 0.6841 (t60) cc_final: 0.6415 (t60) outliers start: 45 outliers final: 23 residues processed: 259 average time/residue: 0.5898 time to fit residues: 167.0818 Evaluate side-chains 253 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN C 108 ASN D 11 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.073939 restraints weight = 17938.282| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.68 r_work: 0.2830 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13590 Z= 0.196 Angle : 0.642 10.123 18498 Z= 0.341 Chirality : 0.044 0.188 2226 Planarity : 0.006 0.088 2328 Dihedral : 5.486 54.481 1886 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.46 % Rotamer: Outliers : 3.12 % Allowed : 18.88 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1773 helix: 1.69 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 150 TYR 0.029 0.002 TYR A 73 PHE 0.016 0.002 PHE F 47 TRP 0.012 0.001 TRP F 127 HIS 0.004 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (13590) covalent geometry : angle 0.64214 / 0.34 (18498) hydrogen bonds : bond 0.05434 / 3.70 ( 888) hydrogen bonds : angle 4.04221 / 2.92 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (mtmt) REVERT: Y 58 MET cc_start: 0.9097 (mmm) cc_final: 0.8556 (mmp) REVERT: Y 125 ASP cc_start: 0.8411 (m-30) cc_final: 0.8161 (m-30) REVERT: Y 244 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8541 (ttpp) REVERT: Z 60 ASN cc_start: 0.7044 (m-40) cc_final: 0.6592 (t0) REVERT: Z 66 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8226 (mt0) REVERT: Z 187 PHE cc_start: 0.8162 (t80) cc_final: 0.7904 (t80) REVERT: A 29 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6375 (tm) REVERT: B 26 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8187 (mm-30) REVERT: B 47 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (tttp) REVERT: B 172 ASN cc_start: 0.6319 (m-40) cc_final: 0.6082 (m-40) REVERT: D 16 ASN cc_start: 0.8075 (m-40) cc_final: 0.7780 (m-40) REVERT: D 29 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6204 (tm) REVERT: F 95 GLN cc_start: 0.8395 (mp10) cc_final: 0.8131 (mp-120) REVERT: F 183 MET cc_start: 0.6722 (mmm) cc_final: 0.6418 (mmm) REVERT: F 189 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: G 19 TRP cc_start: 0.6831 (t60) cc_final: 0.6382 (t60) outliers start: 43 outliers final: 29 residues processed: 257 average time/residue: 0.5721 time to fit residues: 161.2364 Evaluate side-chains 254 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 174 ILE Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 4 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 110 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074477 restraints weight = 18092.276| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.69 r_work: 0.2842 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 13590 Z= 0.175 Angle : 0.622 10.341 18498 Z= 0.330 Chirality : 0.043 0.177 2226 Planarity : 0.006 0.087 2328 Dihedral : 5.454 55.276 1886 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.51 % Rotamer: Outliers : 3.41 % Allowed : 18.74 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1773 helix: 1.74 (0.15), residues: 1326 sheet: None (None), residues: 0 loop : -2.33 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.027 0.002 TYR A 73 PHE 0.015 0.001 PHE F 47 TRP 0.009 0.001 TRP F 127 HIS 0.003 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (13590) covalent geometry : angle 0.62181 / 0.33 (18498) hydrogen bonds : bond 0.05194 / 3.54 ( 888) hydrogen bonds : angle 4.01084 / 2.89 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8389 (mtmt) REVERT: Y 58 MET cc_start: 0.9104 (mmm) cc_final: 0.8552 (mmp) REVERT: Y 125 ASP cc_start: 0.8401 (m-30) cc_final: 0.8147 (m-30) REVERT: Y 244 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8604 (ttpp) REVERT: Z 61 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7380 (p0) REVERT: Z 66 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8235 (mt0) REVERT: Z 187 PHE cc_start: 0.8165 (t80) cc_final: 0.7904 (t80) REVERT: A 29 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6383 (tm) REVERT: B 26 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 47 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8340 (tttp) REVERT: B 172 ASN cc_start: 0.6323 (m-40) cc_final: 0.6053 (m-40) REVERT: D 16 ASN cc_start: 0.8071 (m-40) cc_final: 0.7775 (m-40) REVERT: D 29 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6167 (tm) REVERT: F 95 GLN cc_start: 0.8395 (mp10) cc_final: 0.8136 (mp-120) REVERT: F 183 MET cc_start: 0.6756 (mmm) cc_final: 0.6473 (mmm) REVERT: F 189 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: G 19 TRP cc_start: 0.6838 (t60) cc_final: 0.6380 (t60) outliers start: 47 outliers final: 26 residues processed: 256 average time/residue: 0.5489 time to fit residues: 153.7619 Evaluate side-chains 251 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 142 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 0.0570 chunk 111 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 60 ASN A 15 ASN C 71 HIS C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076343 restraints weight = 17993.080| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.68 r_work: 0.2876 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13590 Z= 0.144 Angle : 0.592 10.323 18498 Z= 0.314 Chirality : 0.042 0.156 2226 Planarity : 0.006 0.086 2328 Dihedral : 5.368 58.486 1886 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 2.47 % Allowed : 19.61 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1773 helix: 1.85 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -2.36 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.022 0.002 TYR A 73 PHE 0.013 0.001 PHE F 47 TRP 0.008 0.001 TRP Y 138 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13590) covalent geometry : angle 0.59166 / 0.31 (18498) hydrogen bonds : bond 0.04689 / 3.19 ( 888) hydrogen bonds : angle 3.92518 / 2.83 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: Y 47 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8376 (mtmt) REVERT: Y 125 ASP cc_start: 0.8404 (m-30) cc_final: 0.8170 (m-30) REVERT: Y 244 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8339 (ttpp) REVERT: Z 66 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8242 (mt0) REVERT: Z 187 PHE cc_start: 0.8138 (t80) cc_final: 0.7866 (t80) REVERT: A 29 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6284 (tm) REVERT: B 26 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 47 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8346 (tttp) REVERT: B 172 ASN cc_start: 0.6283 (m-40) cc_final: 0.6039 (m-40) REVERT: C 260 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8016 (mmtp) REVERT: D 16 ASN cc_start: 0.8117 (m-40) cc_final: 0.7825 (m-40) REVERT: D 29 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6153 (tm) REVERT: F 36 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.7974 (p0) REVERT: F 95 GLN cc_start: 0.8391 (mp10) cc_final: 0.8083 (mp-120) REVERT: F 183 MET cc_start: 0.6757 (mmm) cc_final: 0.6509 (mmm) REVERT: F 189 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7572 (pt0) REVERT: G 19 TRP cc_start: 0.6871 (t60) cc_final: 0.6424 (t60) outliers start: 34 outliers final: 24 residues processed: 252 average time/residue: 0.5263 time to fit residues: 145.0704 Evaluate side-chains 249 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 47 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 244 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 36 ASN Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 175 LYS Chi-restraints excluded: chain Z residue 223 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 29 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.0470 chunk 31 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 169 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 60 ASN A 15 ASN C 108 ASN D 15 ASN F 36 ASN F 108 ASN G 11 ASN G 15 ASN G 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.076725 restraints weight = 18057.815| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.68 r_work: 0.2884 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 13590 Z= 0.144 Angle : 0.595 10.399 18498 Z= 0.314 Chirality : 0.042 0.163 2226 Planarity : 0.006 0.081 2328 Dihedral : 5.312 59.070 1886 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer: Outliers : 2.83 % Allowed : 19.32 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1773 helix: 1.89 (0.15), residues: 1329 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 221 TYR 0.022 0.002 TYR A 73 PHE 0.013 0.001 PHE F 47 TRP 0.008 0.001 TRP Y 138 HIS 0.002 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13590) covalent geometry : angle 0.59545 / 0.31 (18498) hydrogen bonds : bond 0.04632 / 3.14 ( 888) hydrogen bonds : angle 3.90130 / 2.81 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5710.24 seconds wall clock time: 97 minutes 55.27 seconds (5875.27 seconds total)